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Roux, A., Talon, R., Alsalman, Z., Engilberge, S., D'Aleo, A., Di Pietro, S., Robin, A., Bartocci, A., Pilet, G., Dumont, E., Wagner, T., Shima, S., Riobé, F., Girard, E., Maury, O. (2021)
Influence of divalent cations in the protein crystallization process assisted by Lanthanide-based additives. Inorg. Chem. In press.

Watanabe, T., Pfeil-Gardiner, O., Kahnt, J., Koch, J., Shima, S.*, Murphy, B.J.* (2021)
Three-megadalton complex of methanogenic electron-bifurcating and CO2-fixing enzymes. Science 373, 1151-1156. doi: 10.1126/science.abg5550

Pan, H.-J., Huang, G., Wodrich, M.D., Tirani, F.F., Ataka, K., Shima, S.,* Hu, X* (2021)

Diversifying metal-ligand cooperative catalysis in semi-synthetic [Mn]-hydrogenases. Angew. Chem. Int. Ed. 60, 13350 –13357. doi: 10.1002/anie.202100443.

Shima, S., Thauer, R.K. (2021)
Methanothermobacter – Mikrobe des Jahres 2021: Biokatalysator für die Energiewende. BIOSpektrum 27, 14–17 doi: 10.1007/s12268-021-1530-8.

Watanabe, T., Shima, S. (2021)
MvhB-type polyferredoxin as an electron-transfer chain in putative redox-enzyme complexes. Chem. Lett. 50, 353–360, doi: 10.1246/cl.200774.


Huang, G., Arriaza-Gallardo, F.J., Wagner, T., Shima S. (2020)
Crystal structures of [Fe]-hydrogenase from Methanolacinia paynteri suggest a path of the FeGP-cofactor incorporation process. Inorganics 8, 50, doi:10.3390/inorganics8090050.

Engilberge, S., Wagner, T., Carpentier, P., Girarde, E. and Shima, S. (2020)
Krypton-derivatization highlights O2-channeling in a four-electron reducing oxidase. Chem. Comm. 56, 10863-10866 doi: 10.1039/D0CC04557H. 

Shima, S., Huang, G., Wagner, T., Ermler, U. (2020)
Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 74,713–733 doi: 10.1146/annurev-micro-011720-122807.

Huang, G, Wagner, T, Ermler, U, Shima, S. (2020)
Methanogenesis involves direct hydride transfer from H2 to an organic substrate. Nat Rev Chem. 4, 213–221 doi: 10.1038/s41570-020-0167-2.

Huang G, Wagner T, Demmer U, Warkentin E, Ermler U, Shima S. (2020)
The hydride transfer process in NADP-dependent methylene-tetrahydromethanopterin dehydrogenase. J Mol Biol 432, 2042-2054. doi: 10.1016/j.jmb.2020.01.042. 


Hemmann JL, Wagner T, Shima S, Vorholt JA. (2019)
Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc Natl Acad Sci U S A. 116: 25583–25590. DOI: 10.1073/pnas.1911595116. 

Ilina Y., Lorent C., Katz S., Jeoung JH., Shima S., Horch M., Zebger I., Dobbek H. (2019)
X-ray Crystallography and Vibrational Spectroscopy Reveal Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] hydrogenases. Angew Chem Int Ed Engl. 58:18710-18714. doi: 10.1002/anie.201908258. 

Huang, G., Wagner, T., Wodrich, M.D., Ataka, K. Bill, E., Ermler, U., Hu, X. & Shima, S. (2019)
The atomic-resolution crystal structure of activated [Fe]-hydrogenase. Nat. Catal. 2, 537–543, DOI: /10.1038/s41929-019-0289-4.

Pan, H-J, Huang, G., Wodrich, M.D. Tirani, F.F. Ataka, K., Shima, S.* & Hu, X.* (2019) 
A catalytically active [Mn]-hydrogenase incorporating a non-native metal cofactor. Nat. Chem. 11: 669–675. DOI: 10.1038/s41557-019-0266-1.

Engilberge, S., Wagner, T., Santoni, G., Breyton, C., Shima, S., Franzetti, B., Riobé, F., Mauryd, O. & Girard, E. (2019)
Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J. Appl. Crystalogr. 52: 722-731. 

Vögeli, B., Shima, S., Erb, T. & Wagner, T (2019)
Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme. FEBS Lett. 593, 543–553, DOI: 10.1002/1873-3468.13331.

Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U. & Shima, S. (2019)
The bacterial [Fe]-hydrogenase paralog HmdII uses tetrahydrofolate derivatives as substrates. Angew. Chem. Int. Ed.  58 , 3506 –3510. DOI: 10.1002/anie.201813465


Bernhardsgrütter, I., Vögeli, B., Wagner, T., Peter, D.M., Cortina, N.S., Kahnt, J., Bange, G., Engilberge, S., Girard, E., Riobé, F., Maury, O., Shima, S., Zarzycki, J. & Erb, T.J. (2018)
The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat. Chem. Biol. 14,  1127–1132, DOI: 10.1038/s41589-018-0153-x.

Wagner, T., Huang. G., Ermler, U. & Shima, S. (2018) 
How [Fe]-hydrogenase from Methanothermobacter is protected against light and oxidative stress. Angew. Chem. Int. Ed. 57, 15056-15059, DOI: 10.1002/anie.201807203.

Vögeli, B., Rosenthal, R.G., Stoffel, G.M.M., Wagner, T., Kiefer, P., Cortina, N.S., Shima, S. & Erb, T.J. (2018)
InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis. J. Biol. Chem. 293, 17200-17207, DOI: 10.1074/jbc.RA118.005405

Engilberge. S., Riobé, F., Wagner, T., Di Pietro, S., Breyton, C., Franzetti, B., Shima, S., Girard, E., Dumont, E. & Maury, O. (2018)
Unveiling the binding modes of the crystallophore, a terbium-based nucleating and phasing molecular agent for protein crystallography. Chem. Eur. J. 24:9739-9746, DOI: 10.1002/chem.201802172.

Vögeli, B., Engilberge, S., Girard, E., Riobé, F., Maury, O., Erb, T. J., Shima, S. & Wagner, T. (2018)
The archaeal acetoacetyl-CoA-thiolase/HMG-CoA-synthase complex channels the intermediate via a fused CoA-binding site. Pros. Natl. Acad. Sci. USA 115, 3380-3385. DOI: 10.1073/pnas.1718649115.

Huang, G., Wagner, T., Ermler, U. Bill, E., Ataka, K. & Shima, S. (2018)
Dioxygen sensitivity of [Fe]-hydrogenase in the presence of reducing substrates. Angew. Chem. Int. Ed. 57, 4917-4920. DOI: 110.1002/anie.201712293

Wagner, T., Ermler, U. & Shima, S. (2018)
Tungsten-containing formylmethanofuran dehydrogenase. In Encyclopedia of Inorganic and Bioinorganic Chemistry (online). (A. Messerschmidt, Albrecht ed.) John Wiley and Sons, Inc..

Wagner, T., Watanabe, T. & Shima, S. (2018)
Hydrogenotrophic methanogenesis. In Handbook of Hydrocarbon and Lipid Microbiology Series. Biogenesis of Hydrocarbons (A.J.M. Stams and D.Z. Sousa eds.) Springer, Germany.


Wagner, T., Koch, J., Ermler, U. & Shima, S. (2017)
Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science  357, 699–703. 

Bai, L., Wagner, T., Xu, T., Hu, X., Ermler, U. & Shima, S. (2017)
Water-bridged H-bonding network contributes to the catalysis of a SAM-dependent C-methyltransferase HcgC. Angew. Chem. Int. Ed.  56, 10806–0809.

Wagner, T., Wegner, C.-E., Kahnt, J., Ermler, U. & Shima, S. (2017)
Phylogenetic and structural comparisons of the three types of methyl-coenzyme M reductase from Methanococcales and Methanobacteriales. J. Bacteriol.  199, e00197-17 .

Rosenthal, R.G., Vögeli, B., Wagner, T., Shima, S. & Erb, T.J. (2017)
A conserved threonine prevents self-intoxication of enoyl-thioester reductases. Nat. Chem. Biol. 13, 745-749.

Bai, L., Fujishiro, T., Huang, G., Koch, J., Takabayashi, A., Yokono, M., Tanaka, A., Xu, T., Hu, X., Ermler, U. & Shima, S. (2017)
Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semisynthetic hydrogenase. Faraday Discussion, 198, 37-58.

Scheller, S., Ermler, U. & Shima, S. (2017) 
Catabolic pathways & enzymes involved in the anaerobic oxidation of methane. In 6-volume Handbook of Hydrocarbon and Lipid Microbiology (M. Boll ed.) Springer, Germany.

Shima, S. (2017) 
Methanogenic metabolisms. In Archaea Biology (Y. Ishino and H. Atomi Eds) Kyoritsu-Shuppan.


Wagner, T., Ermler, U. & shima, S. (2016)
The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354, 114-117.

Wagner, T., Kahnt, J., Ermler, U. & Shima, S. (2016) 
Didehydroaspartate modification in methyl-coenzyme M reductase catalyzing methane formation. Angew. Chem. Int. Ed. 55, 10630-10633.

Upadhyay, V., Ceh, K., Tumulka, F., Abele, R., Hoffmann, J., Langer, J., Shima, S. & Ermler, U. (2016) 
Molecular characterization of methanogenic N5-methyl-tetrahydromethanopterin: coenzyme M methyltransferase. Biochim. Biophys. Acta. 1858, 2140-2144.

Fujishiro, T., Bai, L., Xu, T., Xie, X., Schick, M. Kahnt, J., Rother, M., Hu, X., Ermler, U. & Shima, S. (2016)
Identification of HcgC as SAM-dependent pyridinol methyltransferase in [Fe]-hydrogenase cofactor biosynthesis. Angew. Chem. Int. Ed. 55, 9648-9651.

Wagner, T., Ermler, U. & Shima, S. (2016)
MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode. Sci. Rep. 6, 28226. doi: 10.1038/srep28226.

Duin, E.C., Wagner, T., Shima, S., Prakash, D., Cronin, B., Yáñez-Ruiz, D.R., Duval, S., Ruembeli, R., Stemmler, R.T., Thauer, R.K. & Kindermann, M. (2016)
Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. Proc. Natl. Acad. Sci. USA, 113, 6172-6177.

Shima, S (2016)
[Highlight] The biological methane-forming reaction: Mechanism confirmed through spectroscopic characterization of key intermediate. Angew. Chem. Int. Ed. 55,13648-13649.

Shima, S. & Fujishiro, T. (2016)
Identification of the biosynthetic enzymes of the [Fe]-hydrogenase cofactor based on the crystal structure of the proteins. Kouso-kogaku News, 76, 26-30.


Shima, S., Chen, D., Xu, X., Wodrich, M.D., Fujishiro, T., Schultz, K.M., Kahnt, J., Ataka, K. & Hu, X. (2015)
Reconstitution of [Fe]-hydrogenase using model complexes. Nat. Chem. 7, 995-1002.

Fujishiro, T., Kahnt, J., Ermler, U. & Shima, S. (2015)
Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor, Nat. Commun. 6, 6895, doi:10.1038/ncomms7895.

Hidese, R., Ataka, K., Bill. E. & Shima, S. (2015)
CuI and H2O2 inactivate and FeII inhibits [Fe]-hydrogenase at very low concentrations. ChemBioChem 16, 1861-1865.

Fujishiro, T., Ataka, K., Ermler, U. & Shima, S. (2015)
Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs. FEBS J. 282 3412–3423.

282, 3412-3423. Doi: 10.1111/febs.13351.

Shima, S. (2015)
An energy metabolism under anoxic conditions: Enzyme chemistry of methanogenesis. Kagakutokogyo 68, 706-708.

Shima, S., Fujishiro, T. & Ermler, U. (2015)
Structure and function of [Fe]-hydrogenase and biosynthesis of the FeGP cofactor. In Biohydrogen (M. Roegner ed.) DE Gruyter, Berlin, Germany.


Kojima, H., Moll, J., Kahnt, J., Fukui, M. & Shima, S. (2014)
A reversed genetic approach reveals the coenzyme specificity and other catalytic properties of three enzymes putatively involved in anaerobic oxidation of methane with sulfate. Environ. Microbiol. 16, 3431-3442.

Fujishiro, T., Ermler U. & Shima, S. (2014)
A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis. FEBS Lett. 588, 2789-2793.

Vitt, S., Ma, K., Warkentin, E., Moll, J., Pierik, A.J., Shima, S. & Ermler, U. (2014)
The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member. J. Mol. Biol. 426, 2813-2826.

Kaneko, M., Takano, Y., Chikaraishi, Y., Ogawa, N.O., Asakawa S., Watanabe, T., Shima, S., Krüger, M., Matsushita, M., Kimura, H. & Ohkouchi, N. (2014)
Quantitative analysis of coenzyme F430 in environmental samples: a new diagnostic tool for methanogenesis and anaerobic methane oxidation. Anal Chem. 86, 3633-3638.

Shima, S. (2014)
Enzyme chemistry of methanogenesis and anaerobic oxidation of methane. Kagakutoseibutsu, 52, 307-312.

Fujishiro, T. & Shima, S. (2014)
Functional analysis based on tertiary structure of proteins. Seibutsukougakukaishi 92, 676.

Shima, S (2014)
Life under anaerobic conditions: Enzymes involved in hydrogenotrophic methanogenesis. In Biomolecules under Extreme Environments. (The Chemical Society of Japan, ed) Kagakudojin, Kyoto, Japan.


Fujishiro, T., Tamura, H., Schick, M., Kahnt, J., Xie, X., Ermler, U. & Shima, S. (2013)
Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis. Angew. Chem. Int. Ed. 52, 12555-12558.

Tamura, H., Salomone-Stagni, M., Fujishiro, T., Warkentin, E., Meyer-Klaucke, W., Ermler, U. & Shima, S. (2013)
Crystal structures of [Fe]-hydrogenase in complex with inhibitory isocyanides: implications for H2-activation site. Angew. Chem. Int. Ed. 52, 9656 -9659 (Selected as a Hot Paper).

Takano, Y., Kaneko, M., Kahnt, J., Imachi, H., Shima, S. & Ohkouchi, M. (2013)
Detection of coenzyme F430 in deep-sea sediments, a key molecule for biological methanogenesis. Organic Geochemistry, 58, 137-140.

Milucka, J., Widdel, F. & Shima, S (2013)
Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia. Environ. Microbiol. 15, 1561-1571.

Mills, D.J., Vitt, S., Strauss, M., Shima, S. & Vonck, J. (2013)
De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. eLife, 2, e00218.



Upadhyay, V., Demmer, U., Warkentin, E., Moll, J. Shima, S. & Ermler, U. (2012)
Structure and catalytic mechanism of N5,N10-methenyltetrahydromethanopterin cyclohydrolase. Biochemistry 51, 8435-8443.

Shima, S. & Ermler, U. (2012)
Crystal structure and biochemistry of methyl-coenzyme M reductase from Black Sea mats mediating anaerobic oxidation of methane. Biseibutsu Seitai 27, 55-62.

Schick, M., Xie, X., Ataka, K., Kahnt, J., Linne, U. & Shima, S. (2012)
Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling. J. Am. Chem. Soc. 134, 3271-3280.

Shima, S., Schick, M., Kahnt, J., Ataka, K., Steinbach, K. & Linne, U. (2012)
Evidence for acyl-iron ligation in the active site of [Fe]-hydrogenase provided by mass spectrometry and infrared spectroscopy. Dalton Trans. 41, 767-771.

Shima, S., Krueger, M., Weinert, T. Demmer, U., Kahnt, J., Thauer, R.K. & Ermler, U. (2012)
Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481, 98-101.


Basen, M., Krüger, M., Milucka, J., Kuever, J., Kahnt, J., Grundmann, O., Meyerdierks, A., Widdel, F. & Shima, S. (2011)
Bacterial enzymes for dissimilatory sulfate reduction in a marine microbial mat (Black Sea) mediating anaerobic oxidation of methane. Environ. Microbiol. 13, 1370-1379

Shima, S., Schick, M. & Tamura, H. (2011)
Preparation of [Fe]-hydrogenase from methanogenic archaea. Methods Enzymol. 494, 119-137.

Shima, S. & Ermler U. (2011)
Structure and function of [Fe]-hydrogenase and its iron-guanylylpyridinol (FeGP) cofactor. Eur. J. Inorg. Chem. 2011, 963-972.

Shima, S. & Ataka, K. (2011)
Isocyanides inhibit [Fe]-hydrogenase with very high affinity. FEBS Lett. 585, 353-356.


Shima, S., Vogt, S., Göbels, A. & Bill E. (2010)
Iron-chromophore circular dichroism of [Fe]-hydrogenase: the conformational change required for H2 activation. Angew. Chem. Int. Ed. 49, 9917-9921.

Thauer, R.K., Kaster, A.-K., Goenrich, M., Schick, M., Hiromoto, T. & Shima, S. (2010)
Hydrogenases from methanogenic archaea, nickel, a novel cofactor and H2-storage. Ann. Rev. Biochem. 79, 507-536.

Salomone-Stagni, M., Stellato, F., Whaley, C.M., Vogt, S., Shima, S., Rauchfuss, T.B., & Meyer-Klaucke, W. (2010)
The iron-site structure of [Fe]-hydrogenase and model systems: an X-ray absorption near edge spectroscopy study. Dalton Trans. 39, 3057-3064.


Ceh, K., Demmer, U., Warkentin, E., Moll, J., Thauer, R.K., Shima, S. & Ermler, U. (2009)
Structural basis of the hydride transfer mechanism in F420 dependent methylene-tetrahydromethanopterin dehydrogenase. Biochemistry 48, 10098-10105.

Hiromoto, T., Warkentin, E., Moll, J., Ermler, U. & Shima, S. (2009)
The crystal structure of an [Fe]-hydrogenase substrate complex reveals the framework for H2-activation. Angew. Chem. Int. Ed. 48, 6457-6460.

Hiromoto, T., Ataka, K., Pilak O., Vogt, S., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., Shima, S., & Ermler, U. (2009)
The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. FEBS Lett. 583, 585-590.

Shima, S., Thauer, R.K. & Ermler, U. (2009)
Carbon monoxide as intrinsic ligands to iron in the active site of [Fe]-hydrogenase. In Metal-carbon bonds in enzymes and cofactors, Vol. 6 of Metal Ions in Life Sciences (Sigel, A., Sigel, H., Sigel, R.K.O., eds). John Wiley &Sons, Ltd, Chichester, UK.


Shima, S (2008)
Functions of methyl-coenzyme M reductase in production and degradation of methane, pp. 182-183. In Applied Microbiology (Kumagai, H., Kato, N., Murata, K. &Sakai, Y., eds) Asakura Shoten, Tokyo, Japan.

Ettwig, K.F., Shima, S., van de Pas-Schoonen, K.T., Kahnt, J., Medema, M., op den Camp, H.J.M. Jetten, M.S.M. & Strous, M (2008)
Denitrifying bacteria oxidize methane in the absence of archaea. Env. Microbiol. 10, 3164-3173.

Shima, S (2008)
The structure of the [Fe]-hydrogenase and the convergent evolution of the active site of hydrogenases. Seikagaku, 80, 846-849.

Shima, S., Pilak O., Vogt, S., Schick, M., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., & Ermler, U. (2008)
The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science, 321, 572-575.

Mayr, S., Latkoczy C., Krüger, M., Günther, D., Shima, S., Thauer, R.K., Widdel, F. & Jaun, B. (2008)
The structure of a F430 variant from archaea associated with anaerobic oxidation of methane. J. Am. Chem. Soc., 130, 10758-10767.

Thauer, R.K. & Shima, S. (2008)
Methane as fuel for anaerobic microorganisms. Ann. NY Acad. Sci. 1125, 158-170.

Guo, Y., Wang, H., Xiao, Y., Vogt, S., Thauer, R.K., Shima, S., Volkers, P.I., Rauchfuss, T.B., Pelmentschikov, V., Case, D.A., Alp, E.E., Sturhahn, W., Yoda, Y. & Cramer, S.P. (2008)
Characterization of the Fe site in the iron-sulfur-cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS). Inorg. Chem., 47, 3969-3977.

Vogt, S., Lyon, E.J., Shima, S. & Thauer, R.K. (2008)
The exchange activities of [Fe]- hydrogenase (iron-sulfurcluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases. J. Biol. Inorg. Chem. 13, 97-106.


Seedorf, H., Hagemeier, C.H., Shima, S., Thauer, R.K., Warkentin, E. & Ermler, U. (2007)
Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic archaea catalyzing the reduction of O2 to H2O. FEBS J. 274, 1588-1599.

Kahnt, J, Buchenau, B., Mahlert, F., Krüger, M., Shima, S. & Thauer, R.K. (2007)
Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea. FEBS J. 274, 4913-4921.

Thauer R.K. & Shima, S. (2007)
Methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. In Archaea (Garrett, R. &Klenk, H.-P., eds) Blackwell Publishing, Inc. Malden, USA, pp 275-283.

Shima, S. & Thauer, R.K. (2007)
A third type of hydrogenase catalyzing H2 activaton. Chem. Rec. 7, 37-46.


Korbas, M., Vogt, S., Meyer-Klaucke, W., Bill, E., Lyon, E.J., Thauer, R.K. & Shima, S. (2006)
The iron-sulfur-cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif. J. Biol. Chem. 281, 30804-30813.

Thauer R.K. & Shima, S. (2006)
Methane and microbes. Nature (News and Views) 440, 878-879.

Shima, S. & Thauer, R.K. (2006)
Anaerobic methane oxidation by archaea: a biochemical approach. Bioscience and Industry, 64, 23-26.

Acharya, P., Warkentin, E., Ermler, U., Thauer, R.K. & Shima, S. (2006)
The structure of formylmethanofuran:tetrahydromethanopterin formyltransferase in complex with its coenzymes. J. Mol. Biol. 357, 870-879.

Thauer R.K. & Shima, S. (2006)
Methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. In Archaea Biology (Garrett, R. &Klenk, H.-P., eds) Blackwell Publishing, Inc. Malden, USA

Pilak, O., Mamat, B., Vogt, S., Hagemeier, C.H., Thauer, R.K., Shima, S., Vonrhein, C., Warkentin, E. & Ermler, U. (2006)
The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd). J. Mol. Biol. 358, 798-809.


Shima, S. & Thauer, R.K. (2005)
Methyl-coenzyme M reductase (MCR) and the anaerobic oxidation of methane (AOM) in methanotrophic archaea. Curr. Opin. Microbiol. 8, 643-648.

Shima, S., Lyon, E.J., Thauer, R.K. Mienert, B. & Bill, E (2005)
Mössbauer studies of the iron-sulfur-cluster-free hydrogenase: the electronic state of the mononuclear Fe active site. J. Am. Chem. Soc. 127, 10430-10435.

Aufhammer, S.W., Warkentin, E., Ermler, U., Hagemeier, C.H., Thauer, R.K. & Shima, S. (2005)
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: architecture of the F420/FMN binding site of enzymes within the non-prolyl cis-peptide containing bacterial luciferase family. Protein Sci. 14, 1840-1849.

Warkentin, E., Hagemeier, C.H., Shima, S., Thauer R.K. & Ermler, U. (2005)
The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic superstructure of the selenomethionine-labelled protein crystal structure. Acta Crystallog. Sect. D. 61, 198-202.


Shima, S., Thauer, R.K. & Ermler, U. (2004)
Hyperthermophilic and salt-dependent formyltransferase from Methanopyrus kandleri. Biochem. Soc. Trans. 32, 269-272.

Sakasegawa, S., Hagemeier, C.H., Thauer R.K. Essen, L.-O. & Shima, S. (2004)
Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with unusual NADP+ preference. Protein Sci. 13, 3162-3171.

Lyon, E.J., Shima, S., Boecher, R., Thauer, R.K., Grevels, F.-W., Bill, E., Roseboom, W. & Albracht, S.P.J. (2004)
Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur cluster free hydrogenase (Hmd) as revealed by infrared spectroscopy. J. Am. Chem. Soc. 126, 14239-14248.

Seedorf, H., Dreisbach, A., Hedderich, R., Shima, S. & Thauer, R.K. (2004)
F420H2-oxidase (FprA) from Methanobrevibacter arboriphilus, a novel coenzyme F420 dependent enzyme involved in O2 detoxification. Arch. Microbiol. 182, 126-137.

Shima, S., Lyon, E.J., Sordel-Klippert, Kauß, M., Kahnt, J., Thauer, R.K., Steinbach, K., Xie, X., Verdier, L. & Griesinger, C. (2004)
The cofactor of the iron-sulfur cluster free hydrogenase Hmd: structure of the light-inactivation product. Angew. Chem. Int. Ed. 43, 2547-2551.

Aufhammer, S.W., Warkentin, E., Berk, H., Shima, S., Thauer, R.K. & Ermler, U. (2004)
Coenzyme binding in F420-dependent alcohol dehydrogenase, a member of the bacterial luciferase family. Structure, 12, 361-370.

Lyon, E.J., Shima, S., Buurman, G., Chowdhuri, S., Batschauer, A., Steinbach, K. & Thauer, R.K. (2004)
UV-A/blue light inactivation of the "metal-free" hydrogenase (Hmd) from methanogenic archaea: the enzyme appears to contain functional iron after all. Eur. J. Biochem., 271, 195-204.


Krüger, M., Meyerdierks, A., Frank Oliver Glöckner, F.O., Amann, R., Widdel, F., Kube, M., Reinhardt, R., Kahnt, J., Böcher, R., Thauer, R.K. & Shima, S. (2003)
An conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878-881.

Hagemeier, C.H., Shima, S., Thauer, R.K., Bourenkov, G., Bartunik, H.D. & Ermler, U. (2003)
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure. J. Mol. Biol. 332, 1047-1057.

Hagemeier, C.H., Shima, S., Warkentin, E., Thauer, R.K. & Ermler, U. (2003)
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms. Acta Crystallog. Sect. D 59, 1635-1655.


Mamat, B., Roth, A., Grimm,, C., Ermler, U., Tziatzios, C., Schubert, D., Thauer, R.K. & Shima, S.* (2002)
Crystal structures and enzymatic properties of three formyltransferases from archaea: Environmental adaptation and evolutionary relationship. Protein Sci. 11, 2168−2178.

Shima, S., Warkentin, E., Thauer, R.K. & Ermler, U. (2002)
Structure and function of enzymes involved in the methanogenic pathway utilizing carbon dioxide and molecular hydrogen. J. Biosci. Bioeng. 93, 519−530.

Shima, S. (2002)
Energy metabolism of methanogens, pp. 325-333. in Great development of microorganisms (Imanaka, T., Ed.). NTS inc., Tokyo (in Japanese).


Warkentin, E., Mamat, B., Sordel-Klippert, M., Wicke, M., Thauer, R.K., Iwata, M., Iwata, S.*, Ermler, U.* & Shima, S.* (2001) 
Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound. EMBO J. 20, 6561−6569.

Shima, S.*, Sordel-Klippert, M., Brioukhanov, A., Netrusov, A., Linder, D. and Thauer, R. K. (2001)
Characterization of heme-dependent catalase from Methanobrevibacter arboriphilus. Appl. Environ. Microbiol. 67, 3041−3045.

Grabarse, W., Mahlert, F., Duin, E. C., Goubeaud, M., Shima, S., Thauer, R. K., Lamzin, V. and Ermler, U.* (2001)
On the mechanism of biological methane formation: Structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding. J. Mol. Biol. 309, 315−330. 

Grabarse, W., Shima, S., Mahlert, F., Duin, E.C. & Thauer, R.K. & Ermler, U. (2001)
Methyl-coenzyme M reductase, pp. 897−914. In Handbook of Metalloproteins (Wieghardt, K., Huber, R., Poulos, T.L., Messerschmidt, A.). John Wiley & sons.

Shima, S. & Thauer R.K. (2001)
Tetrahydromethanopterin specific enzymes from Methanopyrus kandleri. Methods Enzymol. 331, 317−353.

Shima, S. & Thauer R.K. (2001)
Tetrahydromethanopterin specific enzymes from Methanopyrus kandleri. Methods Enzymol. 331, 317−353.


Buurman, G., Shima, S. & Thauer, R.K.* (2000)
The metal-free hydrogenase from methanogenic archaea: Evidence for a bound cofactor. FEBS Lett. 485, 200−204.

Shima, S.*, Thauer, R.K., Ermler, U., Durchschlag, H., Tziatzios, C. & Schubert, D. (2000)
A mutation affecting the association equilibrium of formyltransferase from the hyperthermophilic Methanopyrus kandleri and its influence on the enzyme ́s activity and thermostability. Eur. J. Biochem. 267, 6619−6623.

Grabarse, W., Mahlert, F., Shima, S., Thauer, R.K. & Ermler, U.* (2000)
Comparison of three methyl coenzyme M reductase from phylogenetically distant organisms: Unusual amino acid modification, conservation and adaptation. J. Mol. Biol. 303, 329−344. 

Brioukhanov, A., Netrusov, A., Sordel, M., Thauer, R.K. & Shima, S.* (2000)
Protection of Methanosarcina barkeri against oxidative stress: identification and characterization of an iron superoxide dismutase. Arch. Microbiol. 174, 213−216.

Shima, S., Warkentin, E., Grabarse, W., Sordel, M., Wicke, M., Thauer, R.K. & Ermler, U.* (2000)
Structure of coenzyme F420 dependent methylenetetrahydromethanopterin reductase from two methanogenic archaea. J. Mol. Biol. 300, 935−950.

Selmer, T., Kahnt, J., Goubeaud, M., Shima, S., Grabarse, W., Ermler, U & Thauer, R.K.* (2000)
On the biosynthesis of methylated aminoacids in the active site region of methyl- coenzyme M reductase. J. Biol. Chem. 275. 3755−3760.

Grabarse, W., Vaupel, M., Vorholt, J.A., Shima, S., Thauer, R.K. Wittershagen, A., Bourenkov,G., Bartunik, H.D. & Ermler, U.* (1999)
The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri. Struct. Fold. Des. 7, 1257−1268.

Shima, S.*, Netrusov, A., Sordel, M., Wicke, M., Hartmann, G.C. & Thauer, R.K. (1999)
Purification, characterization, and primary structure of a monofunctional catalase from Methanosarcina barkeri. Arch. Microbiol. 171, 317−323.

Shima, S.*, Tziatzios, C., Schubert, D., Fukada, H., Takahashi, K., Ermler, U. & Thauer, R.K. (1998)
Lyotropic-salt-induced changes in monomer/dimer/tetramer association equilibrium of formyltransferase from the hyperthermophilic Methanopyrus kandleri in relation to the activity and thermostability of the enzyme. Eur. J. Biochem. 258, 85−92.

Shima, S., Hérault D.A. Berkessel, A. & Thauer, R.K.* (1998)
Activation and thermostabilization effects of cyclic 2,3-diphosphoglycerate on the enzymes from the hyperthermophilic Methanopyrus kandleri. Arch. Microbiol. 170, 469−472.

Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. & Thauer, R.K. (1998)
Active sites of transition metal enzymes with focus on nickel. Curr. Opin. Struct. Biol. 8 749−758.

Shima, S. (1998)
Mechanisms of methane formation, pp. 190-205. In Y. Koga, and M. Kamekura (eds), Biology of the Archaebacteria. University of Tokyo Press (in Japanese).

Shima, S. (1998)
Unique structures of the enzymes from methanogens. Seibutsu-Kogaku Kaishi 76, 353 (in Japanese).

Shima, S. (1998)
Mechanism of biological methane formation: Structure and function of methyl-coenzyme M reductase. Protein, Nucleic acid and Enzyme 43, 1461−1467 (in Japanese).

Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. & Thauer, R.K. (1998)
Mechanismus der mikrobiellen Methanbildung. Biospektrum 4, 20−24 (in German).

Ermler, U.*, Grabarse, W., Shima, S., Goubeaud, M. & Thauer, R.K. (1997)
Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278, 1457−1462.

Shima, S.*, Goubeaud, M., Vinzenz, D., Thauer, R.K. & Ermler, U.* (1997)
Crystallization and preliminary X-ray diffraction studies of methyl-coenzyme M reductase from Methanobacterium thermoautotrophicum. J. Biochem. (Tokyo) 121, 829−830.

Ermler, U.*, Merckel, M.C., Thauer, R.K. & Shima, S. (1997)
Formylmethanofuran:tetrahydromethanopterin formyltransferase from Methanopyrus kandleri-new insights into salt-dependence and thermostability. Structure 5, 635−646.

Shima, S., Thauer, R.K., Michel, H. & Ermler, U.* (1996)
Crystallization and preliminary X- ray diffraction studies of formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri. Proteins: Structure, Function, and Genetics 26, 118−120.

Kunow, J.*, Shima, S., Vorholt, J. & Thauer, R.K. (1996)
Primary structure and properties of the formyltransferase from the mesophilic Methanosarcina barkeri: Comparison with the enzymes from thermophilic and hyperthermophilic methanogens. Arch. Microbiol. 165, 97−105.


Shima, S., Weiss, D. & Thauer, R.K.* (1995)
Formylmethanofuran: tetrahydromethanopterin formyltransferase (Ftr) from the hyperthermophilic Methanopyrus kandleri: Cloning, sequencing and functional expression of the ftr gene and one step purification of the enzyme overproduced in Escherichia coli. Eur. J. Biochem. 230, 906−913.

Shima, S.*, Yanagi, M. & H. Saiki (1994)
The phylogenetic position of Hydrogenobacter acidophilus based on 16S rRNA sequence analysis. FEMS Microbiol. Lett. 119, 119−122. 

Shima, S.* & Suzuki, K. (1993)
Hydrogenobacter acidophilus sp. nov., a thermophilic, aerobic, hydrogen-oxidizing bacterium requiring elemental sulfur for growth. Int. J. Syst. Bacteriol. 43, 703−708.

Shima, S., Igarashi, Y. & Kodama, T.* (1993)
Purification and properties of two truncated endoglucanases produced in Escherichia coli harbouring Clostridium cellulolyticum endoglucanase gene celCCD. Appl. Microbiol. Biotechnol. 38, 750−754.

Suzuki, K. & Shima, S. (1993)
Hydrogenobacter acidophilus: Is its ancestor a missing-link between the Bacteria and the Archaea? RIKEN Review 3, 3−4 (in Japanese).

Shima, S. (1993)
Cellulases of clostridia: genetics and biochemistry. The Heredity 47, 56−60 (in Japanese).

Shima, S., Igarashi, Y. & Kodama, T.* (1991)
Nucleotide sequence analysis of the endoglucanase-encoding gene, celCCD, of Clostridium cellulolyticum. Gene 104, 33−38.

Shima, S., Igarashi, Y. & Kodama, T.* (1991)
Molecular cloning of a new endoglucanase gene from Clostridium cellulolyticum and its expression in Escherichia coli. Appl. Microbiol. Biotechnol. 35, 233−236.

Shima, S. (1990)
Application of energy-conversion enzymes for hydrogen production and electrodes of fuel cells. Energy forum No. 432, 112 (in Japanese).

Shima, S. (1990)
Production of organic materials by electric energy: Utilization of hydrogen bacteria. Nogyodenka 43, 13−16 (in Japanese).

Shima, S., Kato, J., Igarashi, Y. & Kodama, T.* (1989)
Cloning and expression of a Clostridium cellobioparum cellulase gene and its excretion from Escherichia coli JM109. J. Ferment. Bioeng. 68, 75−78.

Shima, S. (1985)
Utilization of root-nodule bacteria and its ecological problems. Nogyodenka 38, 15−17 (in Japanese).

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